[ome-users] Upgrade problem
Simon Li
s.p.li at dundee.ac.uk
Thu Sep 18 11:01:21 BST 2014
Can you try deleting the OMERO.server-5.0.4-ice34-b43\var directory and seeing if OMERO starts up?
Simon
On 18/09/2014 10:55, "Anatole Chessel" <anatole.chessel at gurdon.cam.ac.uk<mailto:anatole.chessel at gurdon.cam.ac.uk>> wrote:
Actually, I just realised that a bunch of errors/informations are logged in the windows event viewer, which may help diagnose things:
4 information events, from OMERO.master:
-'Berkeley DB: DbEnv "Registry": Unacceptable log file C:\Users\omero\Desktop\OMERO.server-5.0.4-ice34-b43\var\registry\log.0000000001: unsupported log version 19'
-'Berkeley DB: DbEnv "Registry": Invalid log file: log.0000000001: Invalid argument'
-'Berkeley DB: DbEnv "Registry": PANIC: Invalid argument'
-'Berkeley DB: DbEnv "Registry": process-private: unable to find environment'
2 errors events, the first from OMERO.master, the second from Service Control Manager:
-'exception occurred while initializing a communicator:
SharedDbEnv.cpp:619: Freeze::DatabaseException:
DbEnv::open: DB_RUNRECOVERY: Fatal error, run database recovery'
-'The OMERO.master service terminated with service-specific error Incorrect function..'
Hope that helps,
A.
On 17/09/2014 13:57, Anatole Chessel wrote:
Hi all,
I seem to be having the exact same problem. I am trying to upgrade from 4.4 to 5.0.4 on a windows server 2008R2; after trying without success the OME compiled ice3.5/python2.7 64bit (full thread: http://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7629&start=10 in short omero eventually worked but omero.web did not), I tried ice3.4/python2.6 32bits with the same issues as Jason: 'Failed to startup some components after 300 seconds' and no logs, and launching manually gives a logfile with the same error he just reported...
Many thanks,
A.
On 17/09/2014 13:36, Kotecki, Jason wrote:
Josh, attached is the task list. Also, I ran the command for blitz manually and that actually created a log file.
Thanks,
Jason
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Wednesday, September 17, 2014 5:21 AM
To: Kotecki, Jason
Cc: Simon Li; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
On Sep 16, 2014, at 9:10 PM, Kotecki, Jason wrote:
I just performed the following procedure still with no luck.
Hi Jason,
Sorry about the continued troubles.
......
This instance was upgraded from a version 4.x to version 5.0.2. Would that make a difference?
Possibly, but there should still be some indication of what's going wrong. I assume there's still no log file under var\log\Blitz-0.log?
If there's not, then the only things I can think to check are:
1) are any processes currently running?
Could you send us a process listing? Either using procexp from Sysinternals ( http://scanmail.trustwave.com/?c=129&d=8NKZ1L9jDCHt-Aic-p4xTcOqd5mDInJOXMXxx-2lJA&u=http%3a%2f%2ftechnet%2emicrosoft%2ecom%2fen-us%2fsysinternals%2fbb896653 ) or minimally with "tasklist /v". You can copy the output to the clipboard via "tasklist /v | clip".
2) what is output if you try running the Java command manually? Something like:
C:\windows\system32\java.exe -Xmx2560m -XX:MaxPermSize=256m -Djava.awt.headless=true -Dlogback.configurationFile=c:\\OMERO.server\\etc\\logback.xml -Domero.logfile=c:\\OMERO.server\\var\\log\\${omero.name}.log -Domero.logbase=/OMERO/ManagedRepository/ -Domero.name=Blitz-0 -jar c:\\OMERO.server\\lib\\server\\blitz.jar --Ice.Config=c:\OMERO.server\var\master/servers/Blitz-0/config/config
Cheers,
~Josh.
Best regards,
Jason Kotecki
-----Original Message-----
From: Simon Li [mailto:s.p.li at dundee.ac.uk]
Sent: Monday, September 15, 2014 12:31 PM
To: Kotecki, Jason; Josh Moore
Cc: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
Hi Jason
Have you managed to get any further with this? An upgrade from 5.0.2
to
5.0.4 hasn¹t shown any obvious problems here on Windows. If not, could
you run
sc query state= all type= service
At a command prompt and see if OMERO.master is listed (I wouldn¹t expect it to be if Blitz failed to start, if it is post the relevant output).
Then perhaps try a reboot and a fresh install: rename your existing 5.0.4 server directory, unzip a fresh server, then run bin\omero config set Š individually for each config line instead of copying an existing config.xml file.
Cheers
Simon
On 11/09/2014 20:48, "Kotecki, Jason" <Jason.Kotecki at vai.org><mailto:Jason.Kotecki at vai.org> wrote:
Sorry. Here is the correct diags file.
-Jason
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Thursday, September 11, 2014 3:44 PM
To: Kotecki, Jason
Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
On Sep 11, 2014, at 9:39 PM, Kotecki, Jason wrote:
Here you go. Thanks for your help.
It's interesting that Blitz is now running:
Server: Blitz-0 active (pid = 2416, enabled)
but there's still no log file:
Log files: Blitz-0.log n/a
Is the service bouncing? (i.e. the pid changing frequently)
~J.
-Jason
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Thursday, September 11, 2014 3:37 PM
To: Kotecki, Jason
Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
And one last data point for the evening with the hopes that I'll be
more creative in the morning: could you send the current output of
bin\omero admin diagnostics
Thanks,
~Josh.
On Sep 11, 2014, at 9:31 PM, Kotecki, Jason wrote:
The only errors in the event log are related to the 'ISAPI Filter
or Extension'.
-Jason
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Thursday, September 11, 2014 3:09 PM
To: Kotecki, Jason
Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
On Sep 11, 2014, at 8:40 PM, Kotecki, Jason wrote:
I followed your instructions and had the same result. I attached
the two XML files.
-Jason
Hmmm....both of the files are well-formed. Is there a new event in
the EventViewer of the form:
failed to deploy application
`C:\OMERO.server\etc\grid\windefault.xml':
DescriptorParser.cpp:781: IceXML::ParserException error in
<C:/OMERO.server/etc/grid/generated.xml> descriptor, line 1,
column
161:
duplicate property set `Blitz'
since I certainly only see <properties id="Blitz"> once in your
generated.xml now.
Thanks for the sleuthing,
~Josh.
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Thursday, September 11, 2014 2:21 PM
To: Kotecki, Jason
Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
On Sep 11, 2014, at 8:03 PM, Kotecki, Jason wrote:
Josh, I deleted the generated.xml and tried starting Omero.
Unfortunately the result is the same.
And this is with the config.xml copied from your earlier
installation? If so, could you try:
* (working install) bin\omero config get > config.properties
* (broken install) delete both config.xml and generated.xml
* (broken install) bin\omero config load config.properties
* (broken install) bin\omero admin start
I'm wondering if something has happened with the line-endings
which is causing the XML generation to fail. (You could also send
the two XML files for investigation if there are no sensitive
passwords in the them).
Cheers,
~Josh.
-Jason
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Thursday, September 11, 2014 10:55 AM
To: Kotecki, Jason
Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
On Sep 11, 2014, at 4:52 PM, Kotecki, Jason wrote:
Josh, when I run in foreground mode this is what I see:
C:\OMERO.server\bin>omero admin start --foreground No descriptor
given. Using etc\grid\windefault.xml
Which makes sense. No errors, so that's a start.
I just checked the event viewer and I do see a warning from
'OMERO.master':
The description for Event ID 0 from source OMERO.master cannot
be found. Either the component that raises this event is not
installed on your local computer or the installation is corrupted.
You can install or repair the component on the local computer.
If the event originated on another computer, the display
information had to be saved with the event.
The following information was included with the event:
failed to deploy application
`C:\OMERO.server\etc\grid\windefault.xml':
DescriptorParser.cpp:781: IceXML::ParserException error in
<C:/OMERO.server/etc/grid/generated.xml> descriptor, line 1,
column
161:
duplicate property set `Blitz'
Ah, so this is useful. It does seem like your generated.xml is
corrupt. Can you try deleting it and retrying?
There is also an error from 'ISAPI Filter or Extension':
The description for Event ID 4097 from source ISAPI Filter or
Extension cannot be found. Either the component that raises this
event is not installed on your local computer or the
installation is corrupted. You can install or repair the
component on the local computer.
If the event originated on another computer, the display
information had to be saved with the event.
The following information was included with the event:
Failed to import callback module 'omero_web_iis'
Access is denied.
Hmmm.... this is not related, but if it persists, we'll need to
addresss it as well. But first let's get Blitz running.
Thanks for your patience,
~Josh
Thanks,
Jason Kotecki
-----Original Message-----
From: Josh Moore [mailto:josh at glencoesoftware.com]
Sent: Thursday, September 11, 2014 10:35 AM
To: Kotecki, Jason
Cc: Kenneth Gillen; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
Hi Jason,
On Sep 11, 2014, at 3:56 PM, Kotecki, Jason wrote:
Thanks for your help. I have verified the permissions and that
is not the issue. I downloaded version 5.0.3 and I am
experiencing the same problem as 5.0.4. The Blitz.log file is
not created. Did something change from version 5.0.2 that the
services start differently?
Not particularly. As you noticed, though, there is a new file
(generated.xml) which allows us to automatically set JVM
properties from etc/grid/templates.xml. Try bin/omero admin
jvmcfg for the values that the server will use.
I noticed that there is a new xml file in the versions after
5.0.2, /etc/grid/generated.xml. This file has a line related to
blitz with the word 'REPLACEME'. Is this something I need to change?
<property name="REPLACEMENT:blitz" value="REPLACEME" />
You shouldn't need to perform any manual replacement.
Coming late to this thread a couple of questions:
* Have you checked the Windows EventViewer for any errors?
* Did bin\omero admin start --foreground show any errors?
Cheers,
~Josh
Thanks,
Jason
From: Kenneth Gillen [mailto:k.h.gillen at dundee.ac.uk]
Sent: Wednesday, September 10, 2014 10:19 AM
To: Kotecki, Jason; ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Upgrade problem
The only thing I've had trouble with, using that exact
workflow, is not adding the OMERO service user's permissions to
access the new folder c:\OMERO.server after creating it for the
latest OMERO upgrade - worth checking that.
Best,
Kenny
--
Kenneth Gillen
OME System Administrator
Wellcome Trust Centre for Gene Regulation & Expression College
of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow
Street Dundee
DD1 5EH United Kingdom
Tel: +44 (0) 1382 386364
Skype: kennethgillen
http://scanmail.trustwave.com/?c=129&d=47SR1FVGblQi-14COp4zgQSJ
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From: <Kotecki>, Jason
<Jason.Kotecki at vai.org<mailto:Jason.Kotecki at vai.org><mailto:Jason.Kotecki at vai.org><mailto:Jason.Kotecki at vai.org>>
Date: Wednesday, 10 September 2014 15:11
To:
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Subject: [ome-users] Upgrade problem
Hello, I recently attempted the upgrade from 5.0.2 to 5.0.4.
I'm running on a Windows server using IIS. The process I did was:
1. Backup the database
2. Ran 'omero admin stop'
3. Ran 'omero web iis -remove'
4. Renamed the 'Omero.server' folder to 'Omero.server.OLD'
5. Extracted the 'OMERO.server-5.0.4-ice34-b43.zip' to
'Omero.server.
6. Copied the '/etc/grid/config.xml' file from my old folder
to the new folder.
7. Ran 'omero web iis'
8. Ran 'omero admin start'.
Here is the output of that start command:
C:\OMERO.server\bin>omero admin start No descriptor given.
Using etc\grid\windefault.xml Installing OMERO.master Windows service.
Successfully installed OMERO.master Windows service.
Starting OMERO.master Windows service.
Waiting on startup. Use CTRL-C to exit
.............................
Failed to startup some components after 300 seconds Calling "stop"
on remaining components OMERO.master service deleted.
Waiting on shutdown. Use CTRL-C to exit C:\OMERO.server\bin>
I also attached the results of the 'omero admin diagnostics'
command.
Thanks,
Jason Kotecki
<generated.xml><config.xml>
<omero_diags.txt>
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--
Anatole Chessel, PhD
Research associate
University of Cambridge
Tennis Court Road, Cambridge CB2 1PD
tel: +44 (0)1223 334065
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--
Anatole Chessel, PhD
Research associate
University of Cambridge
Tennis Court Road, Cambridge CB2 1PD
tel: +44 (0)1223 334065
The University of Dundee is a registered Scottish Charity, No: SC015096
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